After I have a battle, space or ground the computer really struggles. I make sure I clear or target and cease fire on the fleets. But a 5 day increment really takes sometime. Before the battle everything is fine, during it fine as well.
Any tips or anything I am missing, I do you the auto progressions with auto pulses.
If you have the event window open then close it or change the amount of days or rows that it will show... that will do some to fix this.
Otherwise you can just clear the event DB of all combat oriented logs manually... you can create some script to do that for you or something... I really have not had a huge problem with it so far though.